If you're using the ToString() method on a .NET boolean to send the value to Javascript, try replacing it with something like
(myBoolean ? "true" : "false")
so that it gets sent to Javascript as the appropriate string representation of the required bool value.
EDIT: Note the difference between:
<script type="text/javascript">
var myBoolean = <%= (myBoolean ? "true" : "false") %>;
</script>
and
<script type="text/javascript">
var myBoolean = '<%= (myBoolean ? "true" : "false") %>';
</script>
In the first example, you end up with:
var myBoolean = false;
and that's a literal Boolean false. In the second, you end up with:
var myBoolean = 'false';
and in JavaScript, 'false' is a non-empty string and consequently if evaluated in a Boolean context, it'll be true. Well, true-ish. :)